Re: Large number of simulations in parallel using replica exchange.

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Mon Feb 11 2019 - 21:44:41 CST

Hi,
If you want only to change psf, pdb, output name and the parameter file,
why not simply write a bash script to iteratively create all the inputs and
execute 6000 simulations?.
Best,

On Mon, Feb 11, 2019 at 3:54 PM Dipak Balasaheb Sanap <dipakbs_at_udel.edu>
wrote:

> Hi, I have a simple problem. I need to run large number of short
> simulations in parallel for different systems. And, my conf file has all
> the parameters same except structure, coordinates, parameters and
> outputname. I am planning to use replica exchange with no communication
> among replicas so I can run all of the simulations in single command.
> Something like this, namd2 replica.conf +replicas 6000 which uses just
> exchanges variable parameters and run 6000 simulations in parallel. My
> question is, how can I write replica.conf file to switch the parameters.
> Below is my normal conf file for a single simulation and I have commented
> where I need to switch the variable (variable 1,2,3 and 4). I am aware that
> I need to use myReplica function or something like that. Thank you very
> much.
>
> ##########################################################
> #ADJUSTABLE PARAMETERS ##
> #############################################################
> # Variable 1 and 2, use different psf and pdb file for every replica
> structure input/cg_20_22_psfgen.psf
> coordinates input/cg_20_22_psfgen.pdb
>
> set temperature 310
> #Variable 3, choose output directory for every replica
> set outputname output/iteration1_0.6
>
> firsttimestep 0
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> #Variable 4, change parameter file for every replica.
> parameters input/from-aa_20_22_0.6.par
>
> temperature $temperature
> # Force-Field Parameters
> exclude 1-2
> cutoff 30.0
> switching on
> switchdist 20.0
> pairlistdist 100.0
> hgroupcutoff 0
> # Integrator Parameters
> timestep 100.0
> nonbondedFreq 1
> stepspercycle 20
> dielectric 20
> # Constant Temperature Control
> langevin on
> langevinDamping 2.0
> langevinTemp $temperature
> langevinHydrogen off
> # Output
> outputName $outputname
> restartfreq 400
> dcdfreq 1000
> xstFreq 400
> outputEnergies 400
> outputPressure 400
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # Minimization
> minimize 2000
> reinitvels $temperature
> run 100000
>
>

-- 
Aravinda Munasinghe,

This archive was generated by hypermail 2.1.6 : Sat Sep 14 2019 - 23:20:08 CDT